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Merge pull request #11669 from rmitsch/feature/candidate-generation-by-docs
Prototype: Entity linking with custom KBs
This commit is contained in:
commit
178f259dbd
1
setup.py
1
setup.py
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@ -30,7 +30,6 @@ MOD_NAMES = [
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"spacy.lexeme",
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"spacy.vocab",
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"spacy.attrs",
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"spacy.kb.candidate",
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"spacy.kb.kb",
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"spacy.kb.kb_in_memory",
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"spacy.ml.parser_model",
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|
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@ -957,11 +957,10 @@ class Errors(metaclass=ErrorsWithCodes):
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"case pass an empty list for the previously not specified argument to avoid this error.")
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E1043 = ("Expected None or a value in range [{range_start}, {range_end}] for entity linker threshold, but got "
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"{value}.")
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E1044 = ("Expected `candidates_batch_size` to be >= 1, but got: {value}")
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E1045 = ("Encountered {parent} subclass without `{parent}.{method}` "
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E1044 = ("Encountered {parent} subclass without `{parent}.{method}` "
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"method in '{name}'. If you want to use this method, make "
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"sure it's overwritten on the subclass.")
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E1046 = ("{cls_name} is an abstract class and cannot be instantiated. If you are looking for spaCy's default "
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E1045 = ("{cls_name} is an abstract class and cannot be instantiated. If you are looking for spaCy's default "
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"knowledge base, use `InMemoryLookupKB`.")
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E1047 = ("`find_threshold()` only supports components with a `scorer` attribute.")
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E1048 = ("Got '{unexpected}' as console progress bar type, but expected one of the following: {expected}")
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@ -1,3 +1,5 @@
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from .kb import KnowledgeBase
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from .kb_in_memory import InMemoryLookupKB
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from .candidate import Candidate, get_candidates, get_candidates_batch
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from .candidate import Candidate
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__all__ = ["KnowledgeBase", "InMemoryLookupKB", "Candidate"]
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@ -1,12 +0,0 @@
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from .kb cimport KnowledgeBase
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from libcpp.vector cimport vector
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from ..typedefs cimport hash_t
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# Object used by the Entity Linker that summarizes one entity-alias candidate combination.
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cdef class Candidate:
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cdef readonly KnowledgeBase kb
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cdef hash_t entity_hash
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cdef float entity_freq
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cdef vector[float] entity_vector
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cdef hash_t alias_hash
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cdef float prior_prob
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109
spacy/kb/candidate.py
Normal file
109
spacy/kb/candidate.py
Normal file
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@ -0,0 +1,109 @@
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import abc
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from typing import List, Union, Callable
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class BaseCandidate(abc.ABC):
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"""A `BaseCandidate` object refers to a textual mention (`alias`) that may or may not be resolved
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to a specific `entity_id` from a Knowledge Base. This will be used as input for the entity_id linking
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algorithm which will disambiguate the various candidates to the correct one.
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Each candidate (alias, entity_id) pair is assigned a certain prior probability.
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DOCS: https://spacy.io/api/kb/#candidate-init
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"""
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def __init__(
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self, mention: str, entity_id: Union[int, str], entity_vector: List[float]
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):
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"""Create new instance of `Candidate`. Note: has to be a sub-class, otherwise error will be raised.
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mention (str): Mention text for this candidate.
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entity_id (Union[int, str]): Unique entity ID.
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entity_vector (List[float]): Entity embedding.
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"""
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self._mention = mention
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self._entity_id = entity_id
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self._entity_vector = entity_vector
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@property
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def entity(self) -> Union[int, str]:
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"""RETURNS (Union[int, str]): Entity ID."""
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return self._entity_id
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@property
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@abc.abstractmethod
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def entity_(self) -> str:
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"""RETURNS (str): Entity name."""
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@property
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def mention(self) -> str:
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"""RETURNS (str): Mention."""
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return self._mention
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@property
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def entity_vector(self) -> List[float]:
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"""RETURNS (List[float]): Entity vector."""
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return self._entity_vector
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class Candidate(BaseCandidate):
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"""`Candidate` for InMemoryLookupKBCandidate."""
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def __init__(
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self,
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retrieve_string_from_hash: Callable[[int], str],
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entity_hash: int,
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entity_freq: int,
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entity_vector: List[float],
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alias_hash: int,
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prior_prob: float,
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):
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"""
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retrieve_string_from_hash (Callable[[int], str]): Callable retrieveing entity name from provided entity/vocab
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hash.
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entity_hash (str): Hashed entity name /ID.
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entity_freq (int): Entity frequency in KB corpus.
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entity_vector (List[float]): Entity embedding.
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alias_hash (int): Hashed alias.
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prior_prob (float): Prior probability of entity for this mention - i.e. the probability that, independent of
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the context, this mention resolves to this entity_id in the corpus used to build the knowledge base. In
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cases in which this isn't always possible (e.g.: the corpus to analyse contains mentions that the KB corpus
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doesn't) it might be better to eschew this information and always supply the same value.
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"""
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super().__init__(
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mention=retrieve_string_from_hash(alias_hash),
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entity_id=entity_hash,
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entity_vector=entity_vector,
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)
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self._retrieve_string_from_hash = retrieve_string_from_hash
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self._entity_hash = entity_hash
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self._entity_freq = entity_freq
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self._alias_hash = alias_hash
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self._prior_prob = prior_prob
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@property
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def entity(self) -> int:
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"""RETURNS (int): hash of the entity_id's KB ID/name"""
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return self._entity_hash
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@property
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def entity_(self) -> str:
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"""RETURNS (str): ID/name of this entity_id in the KB"""
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return self._retrieve_string_from_hash(self._entity_hash)
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@property
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def alias(self) -> int:
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"""RETURNS (int): hash of the alias"""
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return self._alias_hash
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@property
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def alias_(self) -> str:
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"""RETURNS (str): ID of the original alias"""
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return self._retrieve_string_from_hash(self._alias_hash)
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@property
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def entity_freq(self) -> float:
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return self._entity_freq
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@property
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def prior_prob(self) -> float:
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"""RETURNS (List[float]): Entity vector."""
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return self._prior_prob
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@ -1,74 +0,0 @@
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# cython: infer_types=True, profile=True
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from typing import Iterable
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from .kb cimport KnowledgeBase
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from ..tokens import Span
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cdef class Candidate:
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"""A `Candidate` object refers to a textual mention (`alias`) that may or may not be resolved
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to a specific `entity` from a Knowledge Base. This will be used as input for the entity linking
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algorithm which will disambiguate the various candidates to the correct one.
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Each candidate (alias, entity) pair is assigned a certain prior probability.
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DOCS: https://spacy.io/api/kb/#candidate-init
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"""
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def __init__(self, KnowledgeBase kb, entity_hash, entity_freq, entity_vector, alias_hash, prior_prob):
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self.kb = kb
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self.entity_hash = entity_hash
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self.entity_freq = entity_freq
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self.entity_vector = entity_vector
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self.alias_hash = alias_hash
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self.prior_prob = prior_prob
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@property
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def entity(self) -> int:
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"""RETURNS (uint64): hash of the entity's KB ID/name"""
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return self.entity_hash
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@property
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def entity_(self) -> str:
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"""RETURNS (str): ID/name of this entity in the KB"""
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return self.kb.vocab.strings[self.entity_hash]
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@property
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def alias(self) -> int:
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"""RETURNS (uint64): hash of the alias"""
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return self.alias_hash
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@property
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def alias_(self) -> str:
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"""RETURNS (str): ID of the original alias"""
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return self.kb.vocab.strings[self.alias_hash]
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@property
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def entity_freq(self) -> float:
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return self.entity_freq
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@property
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def entity_vector(self) -> Iterable[float]:
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return self.entity_vector
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@property
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def prior_prob(self) -> float:
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return self.prior_prob
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def get_candidates(kb: KnowledgeBase, mention: Span) -> Iterable[Candidate]:
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"""
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Return candidate entities for a given mention and fetching appropriate entries from the index.
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kb (KnowledgeBase): Knowledge base to query.
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mention (Span): Entity mention for which to identify candidates.
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RETURNS (Iterable[Candidate]): Identified candidates.
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"""
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return kb.get_candidates(mention)
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def get_candidates_batch(kb: KnowledgeBase, mentions: Iterable[Span]) -> Iterable[Iterable[Candidate]]:
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"""
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Return candidate entities for the given mentions and fetching appropriate entries from the index.
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kb (KnowledgeBase): Knowledge base to query.
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mention (Iterable[Span]): Entity mentions for which to identify candidates.
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RETURNS (Iterable[Iterable[Candidate]]): Identified candidates.
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"""
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return kb.get_candidates_batch(mentions)
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@ -7,4 +7,4 @@ from ..vocab cimport Vocab
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cdef class KnowledgeBase:
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cdef Pool mem
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cdef readonly Vocab vocab
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cdef readonly int64_t entity_vector_length
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cdef public int64_t entity_vector_length
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|
|
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@ -1,11 +1,11 @@
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# cython: infer_types=True, profile=True
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from pathlib import Path
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from typing import Iterable, Tuple, Union
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from typing import Iterable, Tuple, Union, Iterator, TypeVar, Type, Callable
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from cymem.cymem cimport Pool
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from .candidate import Candidate
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from ..tokens import Span
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from ..tokens import Span, SpanGroup, Doc
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from ..util import SimpleFrozenList
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from ..errors import Errors
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@ -18,38 +18,52 @@ cdef class KnowledgeBase:
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DOCS: https://spacy.io/api/kb
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"""
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_KBType = TypeVar("_KBType", bound=KnowledgeBase)
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def __init__(self, vocab: Vocab, entity_vector_length: int):
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"""Create a KnowledgeBase."""
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# Make sure abstract KB is not instantiated.
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if self.__class__ == KnowledgeBase:
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raise TypeError(
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Errors.E1046.format(cls_name=self.__class__.__name__)
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Errors.E1045.format(cls_name=self.__class__.__name__)
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)
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self.vocab = vocab
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self.entity_vector_length = entity_vector_length
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self.mem = Pool()
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def get_candidates_batch(self, mentions: Iterable[Span]) -> Iterable[Iterable[Candidate]]:
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def get_candidates_all(self, mentions: Iterator[SpanGroup]) -> Iterator[Iterable[Iterable[Candidate]]]:
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"""
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Return candidate entities for specified texts. Each candidate defines the entity, the original alias,
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and the prior probability of that alias resolving to that entity.
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If no candidate is found for a given text, an empty list is returned.
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mentions (Iterable[Span]): Mentions for which to get candidates.
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RETURNS (Iterable[Iterable[Candidate]]): Identified candidates.
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Return candidate entities for mentions stored in `ent` attribute in passed docs. Each candidate defines the
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entity, the original alias, and the prior probability of that alias resolving to that entity.
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If no candidate is found for a given mention, an empty list is returned.
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mentions (Iterator[SpanGroup]): Mentions per doc as SpanGroup instance.
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RETURNS (Iterator[Iterable[Iterable[Candidate]]]): Identified candidates per document.
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"""
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for doc_mentions in mentions:
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yield [self.get_candidates(ent_span) for ent_span in doc_mentions]
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@staticmethod
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def get_ents_as_spangroup(doc: Doc, extractor: Union[str, Callable[[Iterable[Span]], Doc]] = "ent") -> SpanGroup:
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"""
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Fetch entities from doc and returns them as a SpanGroup ready to be used in
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`KnowledgeBase.get_candidates_all()`.
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doc (Doc): Doc whose entities should be fetched.
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extractor (Union[str, Callable[[Iterable[Span]], Doc]]): Defines how to retrieve object holding spans
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used to describe entities. This can be a key referring to a property of the doc instance (e.g. "
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"""
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return [self.get_candidates(span) for span in mentions]
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def get_candidates(self, mention: Span) -> Iterable[Candidate]:
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"""
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Return candidate entities for specified text. Each candidate defines the entity, the original alias,
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and the prior probability of that alias resolving to that entity.
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If the no candidate is found for a given text, an empty list is returned.
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Note that doc is not utilized for further context in this implementation.
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mention (Span): Mention for which to get candidates.
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RETURNS (Iterable[Candidate]): Identified candidates.
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"""
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raise NotImplementedError(
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Errors.E1045.format(parent="KnowledgeBase", method="get_candidates", name=self.__name__)
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Errors.E1044.format(parent="KnowledgeBase", method="get_candidates", name=self.__name__)
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)
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def get_vectors(self, entities: Iterable[str]) -> Iterable[Iterable[float]]:
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|
@ -67,7 +81,7 @@ cdef class KnowledgeBase:
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RETURNS (Iterable[float]): Vector for specified entity.
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"""
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raise NotImplementedError(
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Errors.E1045.format(parent="KnowledgeBase", method="get_vector", name=self.__name__)
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Errors.E1044.format(parent="KnowledgeBase", method="get_vector", name=self.__name__)
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)
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def to_bytes(self, **kwargs) -> bytes:
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|
@ -75,7 +89,7 @@ cdef class KnowledgeBase:
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RETURNS (bytes): Current state as binary string.
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"""
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raise NotImplementedError(
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Errors.E1045.format(parent="KnowledgeBase", method="to_bytes", name=self.__name__)
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Errors.E1044.format(parent="KnowledgeBase", method="to_bytes", name=self.__name__)
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)
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def from_bytes(self, bytes_data: bytes, *, exclude: Tuple[str] = tuple()):
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|
@ -84,25 +98,45 @@ cdef class KnowledgeBase:
|
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exclude (Tuple[str]): Properties to exclude when restoring KB.
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"""
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raise NotImplementedError(
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Errors.E1045.format(parent="KnowledgeBase", method="from_bytes", name=self.__name__)
|
||||
Errors.E1044.format(parent="KnowledgeBase", method="from_bytes", name=self.__name__)
|
||||
)
|
||||
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def to_disk(self, path: Union[str, Path], exclude: Iterable[str] = SimpleFrozenList()) -> None:
|
||||
"""
|
||||
Write KnowledgeBase content to disk.
|
||||
"""Write KnowledgeBase content to disk.
|
||||
path (Union[str, Path]): Target file path.
|
||||
exclude (Iterable[str]): List of components to exclude.
|
||||
"""
|
||||
raise NotImplementedError(
|
||||
Errors.E1045.format(parent="KnowledgeBase", method="to_disk", name=self.__name__)
|
||||
Errors.E1044.format(parent="KnowledgeBase", method="to_disk", name=self.__name__)
|
||||
)
|
||||
|
||||
def from_disk(self, path: Union[str, Path], exclude: Iterable[str] = SimpleFrozenList()) -> None:
|
||||
"""
|
||||
Load KnowledgeBase content from disk.
|
||||
"""Load KnowledgeBase content from disk.
|
||||
path (Union[str, Path]): Target file path.
|
||||
exclude (Iterable[str]): List of components to exclude.
|
||||
"""
|
||||
raise NotImplementedError(
|
||||
Errors.E1045.format(parent="KnowledgeBase", method="from_disk", name=self.__name__)
|
||||
Errors.E1044.format(parent="KnowledgeBase", method="from_disk", name=self.__name__)
|
||||
)
|
||||
|
||||
@classmethod
|
||||
def generate_from_disk(
|
||||
cls: Type[_KBType], path: Union[str, Path], exclude: Iterable[str] = SimpleFrozenList()
|
||||
) -> _KBType:
|
||||
"""
|
||||
Factory method for generating KnowledgeBase subclass instance from file.
|
||||
path (Union[str, Path]): Target file path.
|
||||
exclude (Iterable[str]): List of components to exclude.
|
||||
return (_KBType): Instance of KnowledgeBase subclass generated from file.
|
||||
"""
|
||||
raise NotImplementedError(
|
||||
Errors.E1044.format(parent="KnowledgeBase", method="generate_from_disk", name=cls.__name__)
|
||||
)
|
||||
|
||||
def __len__(self) -> int:
|
||||
"""Returns number of entities in the KnowledgeBase.
|
||||
RETURNS (int): Number of entities in the KnowledgeBase.
|
||||
"""
|
||||
raise NotImplementedError(
|
||||
Errors.E1044.format(parent="KnowledgeBase", method="__len__", name=self.__name__)
|
||||
)
|
||||
|
|
|
@ -1,5 +1,5 @@
|
|||
# cython: infer_types=True, profile=True
|
||||
from typing import Iterable, Callable, Dict, Any, Union
|
||||
from typing import Iterable, Callable, Dict, Any, Union, Optional
|
||||
|
||||
import srsly
|
||||
from preshed.maps cimport PreshMap
|
||||
|
@ -11,7 +11,7 @@ from libcpp.vector cimport vector
|
|||
from pathlib import Path
|
||||
import warnings
|
||||
|
||||
from ..tokens import Span
|
||||
from ..tokens import Span, Doc
|
||||
from ..typedefs cimport hash_t
|
||||
from ..errors import Errors, Warnings
|
||||
from .. import util
|
||||
|
@ -49,6 +49,14 @@ cdef class InMemoryLookupKB(KnowledgeBase):
|
|||
def is_empty(self):
|
||||
return len(self) == 0
|
||||
|
||||
@classmethod
|
||||
def generate_from_disk(
|
||||
cls, path: Union[str, Path], exclude: Iterable[str] = SimpleFrozenList()
|
||||
) -> "InMemoryLookupKB":
|
||||
kb = InMemoryLookupKB(vocab=Vocab(strings=["."]), entity_vector_length=1)
|
||||
kb.from_disk(path)
|
||||
return kb
|
||||
|
||||
def __len__(self):
|
||||
return self.get_size_entities()
|
||||
|
||||
|
@ -227,7 +235,7 @@ cdef class InMemoryLookupKB(KnowledgeBase):
|
|||
self._aliases_table[alias_index] = alias_entry
|
||||
|
||||
def get_candidates(self, mention: Span) -> Iterable[Candidate]:
|
||||
return self.get_alias_candidates(mention.text) # type: ignore
|
||||
return self.get_alias_candidates(mention.text)
|
||||
|
||||
def get_alias_candidates(self, str alias) -> Iterable[Candidate]:
|
||||
"""
|
||||
|
@ -241,14 +249,18 @@ cdef class InMemoryLookupKB(KnowledgeBase):
|
|||
alias_index = <int64_t>self._alias_index.get(alias_hash)
|
||||
alias_entry = self._aliases_table[alias_index]
|
||||
|
||||
return [Candidate(kb=self,
|
||||
entity_hash=self._entries[entry_index].entity_hash,
|
||||
entity_freq=self._entries[entry_index].freq,
|
||||
entity_vector=self._vectors_table[self._entries[entry_index].vector_index],
|
||||
alias_hash=alias_hash,
|
||||
prior_prob=prior_prob)
|
||||
for (entry_index, prior_prob) in zip(alias_entry.entry_indices, alias_entry.probs)
|
||||
if entry_index != 0]
|
||||
return [
|
||||
Candidate(
|
||||
retrieve_string_from_hash=self.vocab.strings.__getitem__,
|
||||
entity_hash=self._entries[entry_index].entity_hash,
|
||||
entity_freq=self._entries[entry_index].freq,
|
||||
entity_vector=self._vectors_table[self._entries[entry_index].vector_index],
|
||||
alias_hash=alias_hash,
|
||||
prior_prob=prior_prob
|
||||
)
|
||||
for (entry_index, prior_prob) in zip(alias_entry.entry_indices, alias_entry.probs)
|
||||
if entry_index != 0
|
||||
]
|
||||
|
||||
def get_vector(self, str entity):
|
||||
cdef hash_t entity_hash = self.vocab.strings[entity]
|
||||
|
|
|
@ -1,14 +1,14 @@
|
|||
from pathlib import Path
|
||||
from typing import Optional, Callable, Iterable, List, Tuple
|
||||
from typing import Optional, Callable, Iterable, List, Tuple, Iterator
|
||||
from thinc.types import Floats2d
|
||||
from thinc.api import chain, list2ragged, reduce_mean, residual
|
||||
from thinc.api import Model, Maxout, Linear, tuplify, Ragged
|
||||
|
||||
from ...util import registry
|
||||
from ...kb import KnowledgeBase, InMemoryLookupKB
|
||||
from ...kb import Candidate, get_candidates, get_candidates_batch
|
||||
from ...kb import Candidate
|
||||
from ...vocab import Vocab
|
||||
from ...tokens import Span, Doc
|
||||
from ...tokens import Span, Doc, SpanGroup
|
||||
from ..extract_spans import extract_spans
|
||||
from ...errors import Errors
|
||||
|
||||
|
@ -89,14 +89,6 @@ def load_kb(
|
|||
return kb_from_file
|
||||
|
||||
|
||||
@registry.misc("spacy.EmptyKB.v2")
|
||||
def empty_kb_for_config() -> Callable[[Vocab, int], KnowledgeBase]:
|
||||
def empty_kb_factory(vocab: Vocab, entity_vector_length: int):
|
||||
return InMemoryLookupKB(vocab=vocab, entity_vector_length=entity_vector_length)
|
||||
|
||||
return empty_kb_factory
|
||||
|
||||
|
||||
@registry.misc("spacy.EmptyKB.v1")
|
||||
def empty_kb(
|
||||
entity_vector_length: int,
|
||||
|
@ -107,13 +99,44 @@ def empty_kb(
|
|||
return empty_kb_factory
|
||||
|
||||
|
||||
@registry.misc("spacy.EmptyKB.v2")
|
||||
def empty_kb_for_config() -> Callable[[Vocab, int], KnowledgeBase]:
|
||||
def empty_kb_factory(vocab: Vocab, entity_vector_length: int):
|
||||
return InMemoryLookupKB(vocab=vocab, entity_vector_length=entity_vector_length)
|
||||
|
||||
return empty_kb_factory
|
||||
|
||||
|
||||
def get_candidates(kb: KnowledgeBase, mention: Span) -> Iterable[Candidate]:
|
||||
"""
|
||||
Return candidate entities for a given mention and fetching appropriate entries from the index.
|
||||
kb (KnowledgeBase): Knowledge base to query.
|
||||
mention (Span): Entity mention for which to identify candidates.
|
||||
RETURNS (Iterable[Candidate]): Identified candidates.
|
||||
"""
|
||||
return kb.get_candidates(mention)
|
||||
|
||||
|
||||
def get_candidates_all(
|
||||
kb: KnowledgeBase, mentions: Iterator[SpanGroup]
|
||||
) -> Iterator[Iterable[Iterable[Candidate]]]:
|
||||
"""
|
||||
Return candidate entities for the given mentions and fetching appropriate entries from the index.
|
||||
kb (KnowledgeBase): Knowledge base to query.
|
||||
mentions (Iterator[SpanGroup]): Mentions per doc as SpanGroup instance.
|
||||
RETURNS (Iterator[Iterable[Iterable[Candidate]]]): Identified candidates per document.
|
||||
"""
|
||||
return kb.get_candidates_all(mentions)
|
||||
|
||||
|
||||
@registry.misc("spacy.CandidateGenerator.v1")
|
||||
def create_candidates() -> Callable[[KnowledgeBase, Span], Iterable[Candidate]]:
|
||||
return get_candidates
|
||||
|
||||
|
||||
@registry.misc("spacy.CandidateBatchGenerator.v1")
|
||||
def create_candidates_batch() -> Callable[
|
||||
[KnowledgeBase, Iterable[Span]], Iterable[Iterable[Candidate]]
|
||||
@registry.misc("spacy.CandidateAllGenerator.v1")
|
||||
def create_candidates_all() -> Callable[
|
||||
[KnowledgeBase, Iterator[SpanGroup]],
|
||||
Iterator[Iterable[Iterable[Candidate]]],
|
||||
]:
|
||||
return get_candidates_batch
|
||||
return get_candidates_all
|
||||
|
|
|
@ -1,4 +1,13 @@
|
|||
from typing import Optional, Iterable, Callable, Dict, Union, List, Any
|
||||
from typing import (
|
||||
Optional,
|
||||
Iterable,
|
||||
Callable,
|
||||
Dict,
|
||||
Union,
|
||||
List,
|
||||
Any,
|
||||
Iterator,
|
||||
)
|
||||
from thinc.types import Floats2d
|
||||
from pathlib import Path
|
||||
from itertools import islice
|
||||
|
@ -8,8 +17,7 @@ from thinc.api import CosineDistance, Model, Optimizer, Config
|
|||
from thinc.api import set_dropout_rate
|
||||
|
||||
from ..kb import KnowledgeBase, Candidate
|
||||
from ..ml import empty_kb
|
||||
from ..tokens import Doc, Span
|
||||
from ..tokens import Doc, Span, SpanGroup
|
||||
from .pipe import deserialize_config
|
||||
from .legacy.entity_linker import EntityLinker_v1
|
||||
from .trainable_pipe import TrainablePipe
|
||||
|
@ -53,12 +61,12 @@ DEFAULT_NEL_MODEL = Config().from_str(default_model_config)["model"]
|
|||
"incl_context": True,
|
||||
"entity_vector_length": 64,
|
||||
"get_candidates": {"@misc": "spacy.CandidateGenerator.v1"},
|
||||
"get_candidates_batch": {"@misc": "spacy.CandidateBatchGenerator.v1"},
|
||||
"get_candidates_all": {"@misc": "spacy.CandidateAllGenerator.v1"},
|
||||
"generate_empty_kb": {"@misc": "spacy.EmptyKB.v2"},
|
||||
"overwrite": True,
|
||||
"scorer": {"@scorers": "spacy.entity_linker_scorer.v1"},
|
||||
"use_gold_ents": True,
|
||||
"candidates_batch_size": 1,
|
||||
"candidates_doc_mode": False,
|
||||
"threshold": None,
|
||||
},
|
||||
default_score_weights={
|
||||
|
@ -78,14 +86,14 @@ def make_entity_linker(
|
|||
incl_context: bool,
|
||||
entity_vector_length: int,
|
||||
get_candidates: Callable[[KnowledgeBase, Span], Iterable[Candidate]],
|
||||
get_candidates_batch: Callable[
|
||||
[KnowledgeBase, Iterable[Span]], Iterable[Iterable[Candidate]]
|
||||
get_candidates_all: Callable[
|
||||
[KnowledgeBase, Iterator[SpanGroup]], Iterator[Iterable[Iterable[Candidate]]]
|
||||
],
|
||||
generate_empty_kb: Callable[[Vocab, int], KnowledgeBase],
|
||||
overwrite: bool,
|
||||
scorer: Optional[Callable],
|
||||
use_gold_ents: bool,
|
||||
candidates_batch_size: int,
|
||||
candidates_doc_mode: bool,
|
||||
threshold: Optional[float] = None,
|
||||
):
|
||||
"""Construct an EntityLinker component.
|
||||
|
@ -98,16 +106,18 @@ def make_entity_linker(
|
|||
incl_prior (bool): Whether or not to include prior probabilities from the KB in the model.
|
||||
incl_context (bool): Whether or not to include the local context in the model.
|
||||
entity_vector_length (int): Size of encoding vectors in the KB.
|
||||
get_candidates (Callable[[KnowledgeBase, Span], Iterable[Candidate]]): Function that
|
||||
produces a list of candidates, given a certain knowledge base and a textual mention.
|
||||
get_candidates_batch (
|
||||
Callable[[KnowledgeBase, Iterable[Span]], Iterable[Iterable[Candidate]]], Iterable[Candidate]]
|
||||
): Function that produces a list of candidates, given a certain knowledge base and several textual mentions.
|
||||
get_candidates (Callable[[KnowledgeBase, Span], Iterable[Candidate]]): Function producing a list of
|
||||
candidates, given a certain knowledge base and a textual mention.
|
||||
get_candidates_all (Callable[[KnowledgeBase, Iterator[SpanGroup]], Iterator[Iterable[Iterable[Candidate]]]]):
|
||||
Function producing a list of candidates per document, given a certain knowledge base and several textual
|
||||
documents with textual mentions.
|
||||
generate_empty_kb (Callable[[Vocab, int], KnowledgeBase]): Callable returning empty KnowledgeBase.
|
||||
scorer (Optional[Callable]): The scoring method.
|
||||
use_gold_ents (bool): Whether to copy entities from gold docs or not. If false, another
|
||||
component must provide entity annotations.
|
||||
candidates_batch_size (int): Size of batches for entity candidate generation.
|
||||
candidates_doc_mode (bool): Whether or not to operate candidate generation in doc mode, i.e. to provide a generator
|
||||
yielding entities per document (candidate generator callable is called only once in this case). If False,
|
||||
the candidate generator is called once per entity.
|
||||
threshold (Optional[float]): Confidence threshold for entity predictions. If confidence is below the threshold,
|
||||
prediction is discarded. If None, predictions are not filtered by any threshold.
|
||||
"""
|
||||
|
@ -137,12 +147,12 @@ def make_entity_linker(
|
|||
incl_context=incl_context,
|
||||
entity_vector_length=entity_vector_length,
|
||||
get_candidates=get_candidates,
|
||||
get_candidates_batch=get_candidates_batch,
|
||||
get_candidates_all=get_candidates_all,
|
||||
generate_empty_kb=generate_empty_kb,
|
||||
overwrite=overwrite,
|
||||
scorer=scorer,
|
||||
use_gold_ents=use_gold_ents,
|
||||
candidates_batch_size=candidates_batch_size,
|
||||
candidates_doc_mode=candidates_doc_mode,
|
||||
threshold=threshold,
|
||||
)
|
||||
|
||||
|
@ -176,14 +186,15 @@ class EntityLinker(TrainablePipe):
|
|||
incl_context: bool,
|
||||
entity_vector_length: int,
|
||||
get_candidates: Callable[[KnowledgeBase, Span], Iterable[Candidate]],
|
||||
get_candidates_batch: Callable[
|
||||
[KnowledgeBase, Iterable[Span]], Iterable[Iterable[Candidate]]
|
||||
get_candidates_all: Callable[
|
||||
[KnowledgeBase, Iterator[SpanGroup]],
|
||||
Iterator[Iterable[Iterable[Candidate]]],
|
||||
],
|
||||
generate_empty_kb: Callable[[Vocab, int], KnowledgeBase],
|
||||
overwrite: bool = BACKWARD_OVERWRITE,
|
||||
scorer: Optional[Callable] = entity_linker_score,
|
||||
use_gold_ents: bool,
|
||||
candidates_batch_size: int,
|
||||
candidates_doc_mode: bool,
|
||||
threshold: Optional[float] = None,
|
||||
) -> None:
|
||||
"""Initialize an entity linker.
|
||||
|
@ -197,17 +208,18 @@ class EntityLinker(TrainablePipe):
|
|||
incl_prior (bool): Whether or not to include prior probabilities from the KB in the model.
|
||||
incl_context (bool): Whether or not to include the local context in the model.
|
||||
entity_vector_length (int): Size of encoding vectors in the KB.
|
||||
get_candidates (Callable[[KnowledgeBase, Span], Iterable[Candidate]]): Function that
|
||||
produces a list of candidates, given a certain knowledge base and a textual mention.
|
||||
get_candidates_batch (
|
||||
Callable[[KnowledgeBase, Iterable[Span]], Iterable[Iterable[Candidate]]],
|
||||
Iterable[Candidate]]
|
||||
): Function that produces a list of candidates, given a certain knowledge base and several textual mentions.
|
||||
get_candidates (Callable[[KnowledgeBase, Span], Iterable[Candidate]]): Function producing a list
|
||||
of candidates, given a certain knowledge base and a textual mention.
|
||||
get_candidates_all (Callable[[KnowledgeBase, Iterator[SpanGroup]], Iterator[Iterable[Iterable[Candidate]]]]):
|
||||
Function producing a list of candidates per document, given a certain knowledge base and several textual
|
||||
documents with textual mentions.
|
||||
generate_empty_kb (Callable[[Vocab, int], KnowledgeBase]): Callable returning empty KnowledgeBase.
|
||||
scorer (Optional[Callable]): The scoring method. Defaults to Scorer.score_links.
|
||||
use_gold_ents (bool): Whether to copy entities from gold docs or not. If false, another
|
||||
component must provide entity annotations.
|
||||
candidates_batch_size (int): Size of batches for entity candidate generation.
|
||||
candidates_doc_mode (bool): Whether or not to operate candidate generation in doc mode, i.e. to provide a
|
||||
generator yielding entities per document (candidate generator callable is called only once in this case). If
|
||||
False, the candidate generator is called once per entity.
|
||||
threshold (Optional[float]): Confidence threshold for entity predictions. If confidence is below the
|
||||
threshold, prediction is discarded. If None, predictions are not filtered by any threshold.
|
||||
DOCS: https://spacy.io/api/entitylinker#init
|
||||
|
@ -231,18 +243,16 @@ class EntityLinker(TrainablePipe):
|
|||
self.incl_prior = incl_prior
|
||||
self.incl_context = incl_context
|
||||
self.get_candidates = get_candidates
|
||||
self.get_candidates_batch = get_candidates_batch
|
||||
self.get_candidates_all = get_candidates_all
|
||||
self.generate_empty_kb = generate_empty_kb
|
||||
self.cfg: Dict[str, Any] = {"overwrite": overwrite}
|
||||
self.distance = CosineDistance(normalize=False)
|
||||
self.kb = generate_empty_kb(self.vocab, entity_vector_length)
|
||||
self.scorer = scorer
|
||||
self.use_gold_ents = use_gold_ents
|
||||
self.candidates_batch_size = candidates_batch_size
|
||||
self.candidates_doc_mode = candidates_doc_mode
|
||||
self.threshold = threshold
|
||||
|
||||
if candidates_batch_size < 1:
|
||||
raise ValueError(Errors.E1044)
|
||||
|
||||
def set_kb(self, kb_loader: Callable[[Vocab], KnowledgeBase]):
|
||||
"""Define the KB of this pipe by providing a function that will
|
||||
create it using this object's vocab."""
|
||||
|
@ -319,7 +329,6 @@ class EntityLinker(TrainablePipe):
|
|||
|
||||
If one isn't present, then the update step needs to be skipped.
|
||||
"""
|
||||
|
||||
for eg in examples:
|
||||
for ent in eg.predicted.ents:
|
||||
candidates = list(self.get_candidates(self.kb, ent))
|
||||
|
@ -445,108 +454,125 @@ class EntityLinker(TrainablePipe):
|
|||
return final_kb_ids
|
||||
if isinstance(docs, Doc):
|
||||
docs = [docs]
|
||||
for i, doc in enumerate(docs):
|
||||
if len(doc) == 0:
|
||||
|
||||
docs = list(docs)
|
||||
# Determine which entities are to be ignored due to labels_discard.
|
||||
valid_ent_idx_per_doc = (
|
||||
[
|
||||
idx
|
||||
for idx in range(len(doc.ents))
|
||||
if doc.ents[idx].label_ not in self.labels_discard
|
||||
]
|
||||
for doc in docs
|
||||
if len(doc) and len(doc.ents)
|
||||
)
|
||||
|
||||
# Call candidate generator.
|
||||
if self.candidates_doc_mode:
|
||||
all_ent_cands = self.get_candidates_all(
|
||||
self.kb,
|
||||
(
|
||||
SpanGroup(
|
||||
doc,
|
||||
spans=[doc.ents[idx] for idx in next(valid_ent_idx_per_doc)],
|
||||
)
|
||||
for doc in docs
|
||||
if len(doc) and len(doc.ents)
|
||||
),
|
||||
)
|
||||
else:
|
||||
# Alternative: collect entities the old-fashioned way - by retrieving entities individually.
|
||||
all_ent_cands = (
|
||||
[
|
||||
self.get_candidates(self.kb, doc.ents[idx])
|
||||
for idx in next(valid_ent_idx_per_doc)
|
||||
]
|
||||
for doc in docs
|
||||
if len(doc) and len(doc.ents)
|
||||
)
|
||||
|
||||
for doc_idx, doc in enumerate(docs):
|
||||
if len(doc) == 0 or len(doc.ents) == 0:
|
||||
continue
|
||||
sentences = [s for s in doc.sents]
|
||||
doc_ent_cands = list(next(all_ent_cands))
|
||||
|
||||
# Loop over entities in batches.
|
||||
for ent_idx in range(0, len(doc.ents), self.candidates_batch_size):
|
||||
ent_batch = doc.ents[ent_idx : ent_idx + self.candidates_batch_size]
|
||||
|
||||
# Look up candidate entities.
|
||||
valid_ent_idx = [
|
||||
idx
|
||||
for idx in range(len(ent_batch))
|
||||
if ent_batch[idx].label_ not in self.labels_discard
|
||||
]
|
||||
|
||||
batch_candidates = list(
|
||||
self.get_candidates_batch(
|
||||
self.kb, [ent_batch[idx] for idx in valid_ent_idx]
|
||||
)
|
||||
if self.candidates_batch_size > 1
|
||||
else [
|
||||
self.get_candidates(self.kb, ent_batch[idx])
|
||||
for idx in valid_ent_idx
|
||||
]
|
||||
# Looping over candidate entities for this doc. (TODO: rewrite)
|
||||
for ent_cand_idx, ent in enumerate(doc.ents):
|
||||
assert hasattr(ent, "sents")
|
||||
sents = list(ent.sents)
|
||||
sent_indices = (
|
||||
sentences.index(sents[0]),
|
||||
sentences.index(sents[-1]),
|
||||
)
|
||||
assert sent_indices[1] >= sent_indices[0] >= 0
|
||||
|
||||
# Looping through each entity in batch (TODO: rewrite)
|
||||
for j, ent in enumerate(ent_batch):
|
||||
assert hasattr(ent, "sents")
|
||||
sents = list(ent.sents)
|
||||
sent_indices = (
|
||||
sentences.index(sents[0]),
|
||||
sentences.index(sents[-1]),
|
||||
if self.incl_context:
|
||||
# get n_neighbour sentences, clipped to the length of the document
|
||||
start_sentence = max(0, sent_indices[0] - self.n_sents)
|
||||
end_sentence = min(
|
||||
len(sentences) - 1, sent_indices[1] + self.n_sents
|
||||
)
|
||||
assert sent_indices[1] >= sent_indices[0] >= 0
|
||||
|
||||
if self.incl_context:
|
||||
# get n_neighbour sentences, clipped to the length of the document
|
||||
start_sentence = max(0, sent_indices[0] - self.n_sents)
|
||||
end_sentence = min(
|
||||
len(sentences) - 1, sent_indices[1] + self.n_sents
|
||||
)
|
||||
start_token = sentences[start_sentence].start
|
||||
end_token = sentences[end_sentence].end
|
||||
sent_doc = doc[start_token:end_token].as_doc()
|
||||
|
||||
# currently, the context is the same for each entity in a sentence (should be refined)
|
||||
sentence_encoding = self.model.predict([sent_doc])[0]
|
||||
sentence_encoding_t = sentence_encoding.T
|
||||
sentence_norm = xp.linalg.norm(sentence_encoding_t)
|
||||
entity_count += 1
|
||||
if ent.label_ in self.labels_discard:
|
||||
# ignoring this entity - setting to NIL
|
||||
start_token = sentences[start_sentence].start
|
||||
end_token = sentences[end_sentence].end
|
||||
sent_doc = doc[start_token:end_token].as_doc()
|
||||
# currently, the context is the same for each entity in a sentence (should be refined)
|
||||
sentence_encoding = self.model.predict([sent_doc])[0]
|
||||
sentence_encoding_t = sentence_encoding.T
|
||||
sentence_norm = xp.linalg.norm(sentence_encoding_t)
|
||||
entity_count += 1
|
||||
if ent.label_ in self.labels_discard:
|
||||
# ignoring this entity - setting to NIL
|
||||
final_kb_ids.append(self.NIL)
|
||||
else:
|
||||
candidates = list(doc_ent_cands[ent_cand_idx])
|
||||
if not candidates:
|
||||
# no prediction possible for this entity - setting to NIL
|
||||
final_kb_ids.append(self.NIL)
|
||||
elif len(candidates) == 1 and self.threshold is None:
|
||||
# shortcut for efficiency reasons: take the 1 candidate
|
||||
final_kb_ids.append(candidates[0].entity_)
|
||||
else:
|
||||
candidates = list(batch_candidates[j])
|
||||
if not candidates:
|
||||
# no prediction possible for this entity - setting to NIL
|
||||
final_kb_ids.append(self.NIL)
|
||||
elif len(candidates) == 1 and self.threshold is None:
|
||||
# shortcut for efficiency reasons: take the 1 candidate
|
||||
final_kb_ids.append(candidates[0].entity_)
|
||||
else:
|
||||
random.shuffle(candidates)
|
||||
# set all prior probabilities to 0 if incl_prior=False
|
||||
prior_probs = xp.asarray([c.prior_prob for c in candidates])
|
||||
if not self.incl_prior:
|
||||
prior_probs = xp.asarray([0.0 for _ in candidates])
|
||||
scores = prior_probs
|
||||
# add in similarity from the context
|
||||
if self.incl_context:
|
||||
entity_encodings = xp.asarray(
|
||||
[c.entity_vector for c in candidates]
|
||||
)
|
||||
entity_norm = xp.linalg.norm(entity_encodings, axis=1)
|
||||
if len(entity_encodings) != len(prior_probs):
|
||||
raise RuntimeError(
|
||||
Errors.E147.format(
|
||||
method="predict",
|
||||
msg="vectors not of equal length",
|
||||
)
|
||||
)
|
||||
# cosine similarity
|
||||
sims = xp.dot(entity_encodings, sentence_encoding_t) / (
|
||||
sentence_norm * entity_norm
|
||||
)
|
||||
if sims.shape != prior_probs.shape:
|
||||
raise ValueError(Errors.E161)
|
||||
scores = prior_probs + sims - (prior_probs * sims)
|
||||
final_kb_ids.append(
|
||||
candidates[scores.argmax().item()].entity_
|
||||
if self.threshold is None
|
||||
or scores.max() >= self.threshold
|
||||
else EntityLinker.NIL
|
||||
random.shuffle(candidates)
|
||||
# set all prior probabilities to 0 if incl_prior=False
|
||||
scores = prior_probs = xp.asarray(
|
||||
[
|
||||
c.prior_prob if self.incl_prior else 0.0
|
||||
for c in candidates
|
||||
]
|
||||
)
|
||||
# add in similarity from the context
|
||||
if self.incl_context:
|
||||
entity_encodings = xp.asarray(
|
||||
[c.entity_vector for c in candidates]
|
||||
)
|
||||
entity_norm = xp.linalg.norm(entity_encodings, axis=1)
|
||||
if len(entity_encodings) != len(prior_probs):
|
||||
raise RuntimeError(
|
||||
Errors.E147.format(
|
||||
method="predict",
|
||||
msg="vectors not of equal length",
|
||||
)
|
||||
)
|
||||
# cosine similarity
|
||||
sims = xp.dot(entity_encodings, sentence_encoding_t) / (
|
||||
sentence_norm * entity_norm
|
||||
)
|
||||
if sims.shape != prior_probs.shape:
|
||||
raise ValueError(Errors.E161)
|
||||
scores = prior_probs + sims - (prior_probs * sims)
|
||||
final_kb_ids.append(
|
||||
candidates[scores.argmax().item()].entity_
|
||||
if self.threshold is None or scores.max() >= self.threshold
|
||||
else EntityLinker.NIL
|
||||
)
|
||||
|
||||
if not (len(final_kb_ids) == entity_count):
|
||||
err = Errors.E147.format(
|
||||
method="predict", msg="result variables not of equal length"
|
||||
)
|
||||
raise RuntimeError(err)
|
||||
|
||||
return final_kb_ids
|
||||
|
||||
def set_annotations(self, docs: Iterable[Doc], kb_ids: List[str]) -> None:
|
||||
|
|
|
@ -1,4 +1,4 @@
|
|||
from typing import Callable, Iterable, Dict, Any, Tuple
|
||||
from typing import Callable, Iterable, Dict, Any, Iterator, Tuple
|
||||
|
||||
import pytest
|
||||
from numpy.testing import assert_equal
|
||||
|
@ -6,16 +6,16 @@ from numpy.testing import assert_equal
|
|||
from spacy import registry, util, Language
|
||||
from spacy.attrs import ENT_KB_ID
|
||||
from spacy.compat import pickle
|
||||
from spacy.kb import Candidate, InMemoryLookupKB, get_candidates, KnowledgeBase
|
||||
from spacy.kb import Candidate, InMemoryLookupKB, KnowledgeBase
|
||||
from spacy.lang.en import English
|
||||
from spacy.ml import load_kb
|
||||
from spacy.ml.models.entity_linker import build_span_maker
|
||||
from spacy.ml.models.entity_linker import build_span_maker, get_candidates
|
||||
from spacy.pipeline import EntityLinker
|
||||
from spacy.pipeline.legacy import EntityLinker_v1
|
||||
from spacy.pipeline.tok2vec import DEFAULT_TOK2VEC_MODEL
|
||||
from spacy.scorer import Scorer
|
||||
from spacy.tests.util import make_tempdir
|
||||
from spacy.tokens import Span, Doc
|
||||
from spacy.tokens import Span, Doc, SpanGroup
|
||||
from spacy.training import Example
|
||||
from spacy.util import ensure_path
|
||||
from spacy.vocab import Vocab
|
||||
|
@ -168,7 +168,7 @@ def test_no_entities():
|
|||
{
|
||||
"sent_starts": [1, 0, 0, 0, 0],
|
||||
},
|
||||
)
|
||||
),
|
||||
]
|
||||
nlp = English()
|
||||
vector_length = 3
|
||||
|
@ -489,11 +489,19 @@ def test_el_pipe_configuration(nlp):
|
|||
assert doc[1].ent_kb_id_ == ""
|
||||
assert doc[2].ent_kb_id_ == "Q2"
|
||||
|
||||
def get_lowercased_candidates(kb, span):
|
||||
# Replace the pipe with a new one with with a different candidate generator.
|
||||
|
||||
def get_lowercased_candidates(kb: InMemoryLookupKB, span: Span):
|
||||
return kb.get_alias_candidates(span.text.lower())
|
||||
|
||||
def get_lowercased_candidates_batch(kb, spans):
|
||||
return [get_lowercased_candidates(kb, span) for span in spans]
|
||||
def get_lowercased_candidates_all(
|
||||
kb: InMemoryLookupKB, mentions: Iterator[SpanGroup]
|
||||
):
|
||||
for doc_mentions in mentions:
|
||||
yield [
|
||||
get_lowercased_candidates(kb, doc_mentions[idx])
|
||||
for idx in range(len(doc_mentions))
|
||||
]
|
||||
|
||||
@registry.misc("spacy.LowercaseCandidateGenerator.v1")
|
||||
def create_candidates() -> Callable[
|
||||
|
@ -501,29 +509,40 @@ def test_el_pipe_configuration(nlp):
|
|||
]:
|
||||
return get_lowercased_candidates
|
||||
|
||||
@registry.misc("spacy.LowercaseCandidateBatchGenerator.v1")
|
||||
@registry.misc("spacy.LowercaseCandidateAllGenerator.v1")
|
||||
def create_candidates_batch() -> Callable[
|
||||
[InMemoryLookupKB, Iterable["Span"]], Iterable[Iterable[Candidate]]
|
||||
[InMemoryLookupKB, Iterator[SpanGroup]],
|
||||
Iterator[Iterable[Iterable[Candidate]]],
|
||||
]:
|
||||
return get_lowercased_candidates_batch
|
||||
return get_lowercased_candidates_all
|
||||
|
||||
# replace the pipe with a new one with with a different candidate generator
|
||||
entity_linker = nlp.replace_pipe(
|
||||
"entity_linker",
|
||||
"entity_linker",
|
||||
config={
|
||||
"incl_context": False,
|
||||
"get_candidates": {"@misc": "spacy.LowercaseCandidateGenerator.v1"},
|
||||
"get_candidates_batch": {
|
||||
"@misc": "spacy.LowercaseCandidateBatchGenerator.v1"
|
||||
def test_reconfigured_el(candidates_doc_mode: bool, doc_text: str) -> None:
|
||||
"""Test reconfigured EL for correct results.
|
||||
candidates_doc_mode (bool): candidates_doc_mode in pipe config.
|
||||
doc_text (str): Text to infer.
|
||||
"""
|
||||
_entity_linker = nlp.replace_pipe(
|
||||
"entity_linker",
|
||||
"entity_linker",
|
||||
config={
|
||||
"incl_context": False,
|
||||
"incl_prior": True,
|
||||
"candidates_doc_mode": candidates_doc_mode,
|
||||
"get_candidates": {"@misc": "spacy.LowercaseCandidateGenerator.v1"},
|
||||
"get_candidates_all": {
|
||||
"@misc": "spacy.LowercaseCandidateAllGenerator.v1"
|
||||
},
|
||||
},
|
||||
},
|
||||
)
|
||||
entity_linker.set_kb(create_kb)
|
||||
doc = nlp(text)
|
||||
assert doc[0].ent_kb_id_ == "Q2"
|
||||
assert doc[1].ent_kb_id_ == ""
|
||||
assert doc[2].ent_kb_id_ == "Q2"
|
||||
)
|
||||
_entity_linker.set_kb(create_kb)
|
||||
_doc = nlp(doc_text)
|
||||
assert _doc[0].ent_kb_id_ == "Q2"
|
||||
assert _doc[1].ent_kb_id_ == ""
|
||||
assert _doc[2].ent_kb_id_ == "Q2"
|
||||
|
||||
# Test individual and doc-wise candidate generation.
|
||||
test_reconfigured_el(False, text)
|
||||
test_reconfigured_el(True, text)
|
||||
|
||||
|
||||
def test_nel_nsents(nlp):
|
||||
|
@ -1169,18 +1188,19 @@ def test_threshold(meet_threshold: bool, config: Dict[str, Any]):
|
|||
# create artificial KB
|
||||
mykb = InMemoryLookupKB(vocab, entity_vector_length=3)
|
||||
mykb.add_entity(entity=entity_id, freq=12, entity_vector=[6, -4, 3])
|
||||
mykb.add_alias(
|
||||
alias="Mahler",
|
||||
entities=[entity_id],
|
||||
probabilities=[1 if meet_threshold else 0.01],
|
||||
)
|
||||
mykb.add_alias(alias="Mahler", entities=[entity_id], probabilities=[1])
|
||||
return mykb
|
||||
|
||||
# Create the Entity Linker component and add it to the pipeline
|
||||
entity_linker = nlp.add_pipe(
|
||||
"entity_linker",
|
||||
last=True,
|
||||
config={"threshold": 0.99, "model": config},
|
||||
config={
|
||||
"threshold": None if meet_threshold else 1.0,
|
||||
# Prior for candidate may be 1.0, rendering the our test setting with threshold 1.0 useless otherwise.
|
||||
"incl_prior": meet_threshold,
|
||||
"model": config,
|
||||
},
|
||||
)
|
||||
entity_linker.set_kb(create_kb) # type: ignore
|
||||
nlp.initialize(get_examples=lambda: train_examples)
|
||||
|
@ -1191,7 +1211,7 @@ def test_threshold(meet_threshold: bool, config: Dict[str, Any]):
|
|||
doc = nlp(text)
|
||||
|
||||
assert len(doc.ents) == 1
|
||||
assert doc.ents[0].kb_id_ == entity_id if meet_threshold else EntityLinker.NIL
|
||||
assert doc.ents[0].kb_id_ == (entity_id if meet_threshold else EntityLinker.NIL)
|
||||
|
||||
|
||||
def test_span_maker_forward_with_empty():
|
||||
|
@ -1207,3 +1227,62 @@ def test_span_maker_forward_with_empty():
|
|||
# just to get a model
|
||||
span_maker = build_span_maker()
|
||||
span_maker([doc1, doc2], False)
|
||||
|
||||
|
||||
def test_nel_candidate_processing():
|
||||
"""Test that NEL handles candidate streams correctly in a set of documents with & without entities as well as empty
|
||||
documents.
|
||||
"""
|
||||
train_data = [
|
||||
(
|
||||
"The sky is blue.",
|
||||
{
|
||||
"sent_starts": [1, 0, 0, 0, 0],
|
||||
},
|
||||
),
|
||||
(
|
||||
"They visited New York.",
|
||||
{
|
||||
"sent_starts": [1, 0, 0, 0, 0],
|
||||
"entities": [(13, 21, "GPE")],
|
||||
},
|
||||
),
|
||||
("", {}),
|
||||
(
|
||||
"New York is a city.",
|
||||
{
|
||||
"sent_starts": [1, 0, 0, 0, 0, 0],
|
||||
"entities": [(0, 8, "GPE")],
|
||||
},
|
||||
),
|
||||
]
|
||||
|
||||
nlp = English()
|
||||
nlp.add_pipe("sentencizer")
|
||||
|
||||
vector_length = 3
|
||||
train_examples = []
|
||||
for text, annotation in train_data:
|
||||
train_examples.append(Example.from_dict(nlp(text), annotation))
|
||||
|
||||
def create_kb(vocab):
|
||||
# create artificial KB
|
||||
mykb = InMemoryLookupKB(vocab, entity_vector_length=vector_length)
|
||||
mykb.add_entity(entity="Q60", freq=12, entity_vector=[1, 2, 3])
|
||||
mykb.add_alias("New York", ["Q60"], [0.9])
|
||||
return mykb
|
||||
|
||||
# Create and train the Entity Linker
|
||||
entity_linker = nlp.add_pipe("entity_linker", last=True)
|
||||
entity_linker.set_kb(create_kb)
|
||||
optimizer = nlp.initialize(get_examples=lambda: train_examples)
|
||||
for i in range(2):
|
||||
losses = {}
|
||||
nlp.update(train_examples, sgd=optimizer, losses=losses)
|
||||
|
||||
# Add a custom rule-based component to mimick NER
|
||||
ruler = nlp.add_pipe("entity_ruler", before="entity_linker")
|
||||
ruler.add_patterns([{"label": "GPE", "pattern": [{"LOWER": "new york"}]}]) # type: ignore
|
||||
|
||||
# this will run the pipeline on the examples and shouldn't crash
|
||||
nlp.evaluate(train_examples)
|
||||
|
|
|
@ -2,7 +2,9 @@ from typing import Callable, Protocol, Iterable, Iterator, Optional
|
|||
from typing import Union, Tuple, List, Dict, Any, overload
|
||||
from cymem.cymem import Pool
|
||||
from thinc.types import Floats1d, Floats2d, Ints2d
|
||||
|
||||
from .span import Span
|
||||
from .span_group import SpanGroup
|
||||
from .token import Token
|
||||
from ._dict_proxies import SpanGroups
|
||||
from ._retokenize import Retokenizer
|
||||
|
@ -129,6 +131,7 @@ class Doc:
|
|||
outside: Optional[List[Span]] = ...,
|
||||
default: str = ...
|
||||
) -> None: ...
|
||||
ents_spangroup: SpanGroup
|
||||
@property
|
||||
def noun_chunks(self) -> Iterator[Span]: ...
|
||||
@property
|
||||
|
|
|
@ -19,6 +19,8 @@ import warnings
|
|||
|
||||
from .span cimport Span
|
||||
from .token cimport MISSING_DEP
|
||||
from .span_group cimport SpanGroup
|
||||
|
||||
from ._dict_proxies import SpanGroups
|
||||
from .token cimport Token
|
||||
from ..lexeme cimport Lexeme, EMPTY_LEXEME
|
||||
|
@ -701,6 +703,14 @@ cdef class Doc:
|
|||
"""
|
||||
return self.text
|
||||
|
||||
@property
|
||||
def ents_spangroup(self) -> SpanGroup:
|
||||
"""
|
||||
Returns entities (in `.ents`) as `SpanGroup`.
|
||||
RETURNS (SpanGroup): All entities (in `.ents`) as `SpanGroup`.
|
||||
"""
|
||||
return SpanGroup(self, spans=self.ents, name="ents")
|
||||
|
||||
property ents:
|
||||
"""The named entities in the document. Returns a tuple of named entity
|
||||
`Span` objects, if the entity recognizer has been applied.
|
||||
|
|
Loading…
Reference in New Issue
Block a user